Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Plant Biology; Michigan State University
Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Plant Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Agronomy
Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; USDA-ARS Dairy Forage Research Center, Madison, WI (United States)
Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
Evans, Joseph, et al. "Diversity and population structure of northern switchgrass as revealed through exome capture sequencing." The Plant Journal, vol. 84, no. 4, Oct. 2015. https://doi.org/10.1111/tpj.13041
Evans, Joseph, Crisovan, Emily, Barry, Kerrie, Daum, Chris, Jenkins, Jerry, Kunde-Ramamoorthy, Govindarajan, Nandety, Aruna, Ngan, Chew Yee, Vaillancourt, Brieanne, Wei, Chia-Lin, Schmutz, Jeremy, Kaeppler, Shawn M., Casler, Michael D., & Buell, Carol Robin (2015). Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. The Plant Journal, 84(4). https://doi.org/10.1111/tpj.13041
Evans, Joseph, Crisovan, Emily, Barry, Kerrie, et al., "Diversity and population structure of northern switchgrass as revealed through exome capture sequencing," The Plant Journal 84, no. 4 (2015), https://doi.org/10.1111/tpj.13041
@article{osti_1438259,
author = {Evans, Joseph and Crisovan, Emily and Barry, Kerrie and Daum, Chris and Jenkins, Jerry and Kunde-Ramamoorthy, Govindarajan and Nandety, Aruna and Ngan, Chew Yee and Vaillancourt, Brieanne and Wei, Chia-Lin and others},
title = {Diversity and population structure of northern switchgrass as revealed through exome capture sequencing},
annote = {Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.},
doi = {10.1111/tpj.13041},
url = {https://www.osti.gov/biblio/1438259},
journal = {The Plant Journal},
issn = {ISSN 0960-7412},
number = {4},
volume = {84},
place = {United States},
publisher = {Society for Experimental Biology},
year = {2015},
month = {10}}
Univ. of Wisconsin, Madison, WI (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Michigan State Univ., East Lansing, MI (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
FC02-07ER64494; AC02-05CH11231
OSTI ID:
1438259
Alternate ID(s):
OSTI ID: 1616044
Journal Information:
The Plant Journal, Journal Name: The Plant Journal Journal Issue: 4 Vol. 84; ISSN 0960-7412